On 6 April 1994 someone shot down a plane carrying President Juvenal Habyarimana of Rwanda and Burundian President Cyprien Ntaryamira at it attempted to land at Kigali Airport. Habyarimana’s death sparked waves of killings by Hutu extremists, the Interahamwe militia, and eventually significant numbers of opportunistic collaborators. They targeted not only ethnic Tutsi but also Hutu moderates, particularly supporters of the Arusha Peace Accords. Hundreds of thousands died in the fastest genocide in history; an excess of human remains choked Rwanada’s rivers. The genocide ended only when the Tutsi-dominated Rwandan Patriotic Front (RPF) defeated the government and took control of the country.

Scholars and observers have long speculated about who shot down the plane. Suspicions generally fell on Hutu extremists–and perhaps even the Akazu (“Little House”) of cronies and relatives surrounding Habyarimana and his wife. In other words, those who stood to lose the most from the accords killed the President and initiated a genocide to maintain their hold on power.

But not according to former UN investigator Michael Hourigan, who tells the BBC that the UN halted his investigation into Habyarimana’s death. The reason: he was close to pinning responsibility on Paul Kagame: head of the RPF and now the President of Rwanda. Michael Doyle reports:

The former UN investigator who has now spoken to the BBC, Michael Hourigan, worked on several aspects of the genocide in 1996 and 1997.

He successfully prosecuted a number of Hutu leaders responsible for the mass killings, but also found witnesses who alleged that the Tutsi Paul Kagame, the current president of Rwanda, was involved in the plot to shoot down the plane when he was a rebel leader.

Mr Hourigan told the BBC from his home in Australia that senior UN officials instructed him to stop his enquiries.

“None of it makes sense,” he said.

“That all of a sudden when we get the breakthrough and we start to actually get people coming forward saying: ‘We were involved in the crash, you know, I fired a rocket which took the president’s aircraft down’ – when we’re getting those people with that sort of quality information coming forwards and then we shut it down.”

“I mean it didn’t make sense to me then and it doesn’t make sense to me now.” ….

Senior UN officials say the enquiry into the plane crash was stopped because it was not within the mandate of the genocide tribunal. Mr Hourigan strongly disagrees.

A spokesman for the then chief prosecutor of the tribunal, Louise Arbour, who is now the UN human rights commissioner, said she would not comment on Mr Hourigan’s complaints because she had a duty of confidentiality.

Diplomats say Rwanda would almost certainly have stopped cooperating with the tribunal if its investigations targeted Mr Kagame.

The diplomats add that the foreign policies of western nations towards Rwanda are partly driven by guilt because the international community failed to stop the mass killings.

President Kagame has denied involvement in shooting down the plane, but adds that he does not regret the death of the former Rwandan leader, who he describes as a dictator.

This is a pretty big deal.

When the France’s anti-terrorism judge accused Kagame in November of 2006, it was easy to dismiss his claims. The French government backed the Hutu regime and doesn’t like Kagame’s Anglophone orientation. Chris McGreal of The Guardian explains the case for French bias before he concludes that Hutu extremists were likely responsible for Habyarimana’s death.

When the genocide started, Paris made no secret of where its loyalties lay. The French military flew in ammunition for government forces and, in the following weeks, a stream of Hutu officials travelled to Paris, including Jean-Bosco Barayagwiza, who was later convicted of genocide by the international tribunal, for meetings with President François Mitterrand and the French prime minister. Even as the mass graves filled across Rwanda, Paris engineered the delivery of millions of dollars’ worth of weapons to the Hutu regime from Egypt and South Africa.

Africa has traditionally been considered such a special case in Paris that France’s policy is run out of the presidency. At the time, the “Africa cell” was headed by Mitterrand’s son, Jean-Christophe, a close friend of the Habyarimanas. He later said that there could not have been a genocide because “Africans are not that organised”. France’s president did not deny what had happened, but took a view no less racist: “In such countries, genocide is not too important.”

Hourigan’s accusations suggest, however, that there is more to this than Francophone-sphere political maneuvering.

Let us suppose that Hourigan’s sources are unreliable. I still find it troubling that the UN might have shut down his investigation rather than rattle cooperation from the Kagame government. This sort of behavior brings back memories of how higher-level UN officials behaved immediately before and after the genocide broke out.

At the same time, post-conflict justice must always be tempered by pragmatism. Peace may not be worth any price, but it seldom comes cheap. And no one should shed any tears for Habyarimana.